The main goal of this proposal is to further develop a procedure for the rapid physical mapping of genomes. Clone-Array Pooled Shotgun Indexing ("CAPSI") is a novel method for comparative physical mapping of BACs. CAPSI is carried out by pooling arrayed BAC clones, and generating shotgun sequence pools to appropriate coverage. CAPSI uses this information to map individual BACs onto homologous sequences of a related organism. The first two steps, pooling of BAC clones and shotgun sequencing, draw on existing high throughput methodology at the Baylor Human Genome Sequencing Center. The last step, deconvolution of the pools into specific BACs, is accomplished by comparison of DNA sequence reads from pools against a reference genomic or cDNA sequence of a related organism: if two reads from two different pools match the reference sequence at a close distance, they are both assigned (deconvoluted) to the BAC at the intersection of the two pools and the BAC is mapped onto the region of the reference sequence between the two matches.A specific goal of this proposal is to map 2,404 arrayed BACs of Rattus Norvegicus and 74,752 arrayed BACs of Macaque Mulatta (Rhesus Macaque) (4.24 X random coverage assuming 3Gb genome) onto assembled Human genomic sequence via CAPSI while concurrently developing the CAPSI method.